Yes, Koenig's joke was along the lines of: Chekov is off duty with, ah, stomach problems. Khan has an urgent need to, ah, use the little boy's room, but Chekov is, ah, monopolising it. So when Chekov finally leaves, after Khan's endured an agonisingly long wait, Khan swears that he'll never forget the man who made him suffer so long...

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"Some days are better than others. They say that where I come from."
"Loudly, I imagine, on the day you left."
(Blake's 7 - Rumours of Death)